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Bacterial whole genome sequencing

Carlos M Suligoy, Santiago M Lattar, Mariángeles Noto Llana, Cintia D González, Lucía P Alvarez, D Ashley Robinson, Marisa I Gómez, Fernanda R Buzzola, Daniel O Sordelli
Selection pressures exerted on Staphylococcus aureus by host factors may lead to the emergence of mutants better adapted to the evolving conditions at the infection site. This study was aimed at identifying the changes that occur in S. aureus exposed to the host defense mechanisms during chronic osteomyelitis and evaluating whether these changes affect the virulence of the organism. Genome assessment of two S. aureus isolates collected 13 months apart (HU-85a and HU-85c) from a host with chronic osteomyelitis was made by whole genome sequencing...
2018: Frontiers in Cellular and Infection Microbiology
Tanja Stadler, Dominik Meinel, Lisandra Aguilar-Bultet, Jana S Huisman, Ruth Schindler, Adrian Egli, Helena M B Seth-Smith, Lucas Eichenberger, Peter Brodmann, Philipp Hübner, Claudia Bagutti, Sarah Tschudin-Sutter
INTRODUCTION: Extended-spectrum beta-lactamases (ESBL)-producing Enterobacteriaceae were first described in relation with hospital-acquired infections. In the 2000s, the epidemiology of ESBL-producing organisms changed as especially ESBL-producing Escherichia coli was increasingly described as an important cause of community-acquired infections, supporting the hypothesis that in more recent years ESBL-producing Enterobacteriaceae have probably been imported into hospitals rather than vice versa...
February 17, 2018: BMJ Open
Deepak Kumar, Siddhartha Thakur
Preharvest food safety research and activities have advanced over time with the recognition of the importance and complicated nature of the preharvest phase of food production. In developed nations, implementation of preharvest food safety procedures along with strict monitoring and containment at various postharvest stages such as slaughter, processing, storage, and distribution have remarkably reduced the burden of foodborne pathogens in humans. Early detection and adequate surveillance of pathogens at the preharvest stage is of the utmost importance to ensure a safe meat supply...
February 2018: Microbiology Spectrum
Michael Gétaz, Steve Baeyen, Jochen Blom, Martine Maes, Bart Cottyn, Joël F Pothier
Xanthomonas arboricola pv. fragariae was described in 2001 as the causal agent of strawberry bacterial leaf blight. We report here the first draft whole-genome sequences of five X. arboricola pv. fragariae isolates from Italy and France.
February 15, 2018: Genome Announcements
Jose A Romero-Espinoza, Yazmin Moreno-Valencia, Rodrigo H Coronel-Tellez, Manuel Castillejos-Lopez, Andres Hernandez, Aaron Dominguez, Angel Miliar-Garcia, Arturo Barbachano-Guerrero, Rogelio Perez-Padilla, Alejandro Alejandre-Garcia, Joel A Vazquez-Perez
BACKGROUND: Acute asthma exacerbations and pneumonia are important causes of morbidity and mortality in children and may coexist in the same children, although symptom overlap may lead to difficulties in diagnosis. Microbial and viral diversity and differential abundance of either may play an important role in infection susceptibility and the development of acute and chronic respiratory diseases. OBJECTIVES: To describe the virome and bacteriome present in the upper respiratory tract of hospitalized children with a clinical diagnosis of asthma and pneumonia during an acute exacerbation and an acute respiratory illness ARI episode respectively...
2018: PloS One
Jasmin Cevost, Cédric Vaillant, Sam Meyer, Burkhard Rost
Motivation: Many DNA-binding proteins recognize their target sequences indirectly, by sensing DNA's response to mechanical distortion. ThreaDNA estimates this response based on high-resolution structures of the protein-DNA complex of interest. Implementing an efficient nanoscale modeling of DNA deformations involving essentially no adjustable parameters, it returns the profile of deformation energy along whole genomes, at base-pair resolution, within minutes on usual laptop/desktop computers...
February 15, 2018: Bioinformatics
Geert Cremers, Lavinia Gambelli, Theo van Alen, Laura van Niftrik, Huub J M Op den Camp
With the emergence of Next Generation Sequencing, major advances were made with regard to identifying viruses in natural environments. However, bioinformatical research on viruses is still limited because of the low amounts of viral DNA that can be obtained for analysis. To overcome this limitation, DNA is often amplified with multiple displacement amplification (MDA), which may cause an unavoidable bias. Here, we describe a case study in which the virome of a bioreactor is sequenced using Ion Torrent technology...
2018: PeerJ
James C Wallace, Jessica E Youngblood, Jesse A Port, Alison C Cullen, Marissa N Smith, Tomomi Workman, Elaine M Faustman
Whole-metagenome sequencing (WMS) has emerged as a powerful tool to assess potential public health risks in marine environments by measuring changes in microbial community structure and function in uncultured bacteria. In addition to monitoring public health risks such as antibiotic resistance determinants, it is essential to measure predictors of microbial variation in order to identify natural versus anthropogenic factors as well as to evaluate reproducibility of metagenomic measurements.This study expands our previous metagenomic characterization of Puget Sound by sampling new nearshore environments including the Duwamish River, an EPA superfund site, and the Hood Canal, an area characterized by highly variable oxygen levels...
2018: PloS One
Anna Nilsson, Astrid Skarp, Cecilia Johansson, René Kaden, Lars Engstrand, Hilpi Rautelin
Campylobacter jejuni and Campylobacter coli are important bacterial enteropathogens. Poultry is the best-known reservoir for Campylobacter infection but natural bodies of water have also been shown to be important pathways for transmission. Campylobacter can survive in cold water but most of the studies have focused on C. jejuni only. In this paper, we take a closer look at the biology and water survival strategies of C. coli. Eight C. coli isolates cultivated from raw (incoming) surface water at water plants in Sweden were characterized using whole-genome sequencing and phenotypical assays...
February 9, 2018: MicrobiologyOpen
Mallika Lavania, Itu Singh, Ravindra P Turankar, Anuj Kumar Gupta, Madhvi Ahuja, Vinay Pathak, Utpal Sengupta
Despite more than three decades of multidrug therapy (MDT), leprosy remains a major public health issue in several endemic countries, including India. The emergence of drug resistance in Mycobacterium leprae (M. leprae) is a cause of concern and poses a threat to the leprosy-control program, which might ultimately dampen the achievement of the elimination program of the country. Rifampicin resistance in clinical strains of M. leprae are supposed to arise from harboring bacterial strains with mutations in the 81-bp rifampicin resistance determining region (RRDR) of the rpoB gene...
2018: Infection and Drug Resistance
Raymond S W Tsang, Tauqeer Ahmad, Shaun Tyler, Brigitte Lefebvre, Shelley L Deeks, Rodica Gilca, Linda Hoang, Gregory Tyrrell, Paul Van Caeseele, Gary Van Domselaar, Frances B Jamieson
OBJECTIVE: We analyzed the Canadian invasive MenW ST-11 cc isolates by whole genome typing and compared Canadian isolates with similar isolates elsewhere. METHODS: Whole genome typing of 30 MenW ST-11 cc, 20 meningococcal group C (MenC) ST-11 cc and 31 MenW ST-22 cc isolates were carried out on the Bacterial Isolate Genome Sequence database platform. Canadian MenW ST-11 cc isolates were compared with the 2000 MenW Hajj outbreak strain, as well as with MenW ST-11 cc from other countries...
February 4, 2018: International Journal of Infectious Diseases: IJID
S Peter, D Bezdan, P Oberhettinger, W Vogel, D Dörfel, J Dick, M Marschal, J Liese, C Weidenmaier, I Autenrieth, S Ossowski, M Willmann
Citrobacter species harbouring metallo-beta-lactamases (MBLs) have been reported from various countries and different sources, but their isolation from clinical specimens remains a rare event in Europe. MBL-harbouring Enterobacteriaceae are considered a major threat in infection control as therapeutic options are often limited to colistin. In this study, we applied whole genome sequencing to characterize five clinical isolates of multidrug-resistant Citrobacter werkmanii obtained from rectal swabs. Four strains possessed a class I integron with a novel blaVIM-48 MBL-resistance gene and the aminoglycoside acetyltransferase gene aacA4, while one isolate harboured a blaIMP-8 MBL...
February 2, 2018: International Journal of Antimicrobial Agents
Assia Saltykova, Véronique Wuyts, Wesley Mattheus, Sophie Bertrand, Nancy H C Roosens, Kathleen Marchal, Sigrid C J De Keersmaecker
Whole genome sequencing represents a promising new technology for subtyping of bacterial pathogens. Besides the technological advances which have pushed the approach forward, the last years have been marked by considerable evolution of the whole genome sequencing data analysis methods. Prior to application of the technology as a routine epidemiological typing tool, however, reliable and efficient data analysis strategies need to be identified among the wide variety of the emerged methodologies. In this work, we have compared three existing SNP-based subtyping workflows using a benchmark dataset of 32 Salmonella enterica subsp...
2018: PloS One
Pedro Henrique N Panzenhagen, Claudius C Cabral, Philip N Suffys, Robson M Franco, Dalia P Rodrigues, Carlos A Conte-Junior
Salmonella pathogenicity relies on virulence factors many of which are clustered within the Salmonella pathogenicity islands (SPIs). Salmonella also harbors mobile genetic elements such as virulence plasmids, prophage-like elements and antimicrobial resistance genes which can contribute to increase its pathogenicity. Here, we have genetically characterized a selected S. Typhimurium strain (CCRJ_26) from our previous study with Multiple Drugs Resistant profile and high-frequency PFGE clonal profile which apparently persists in the pork production center of Rio de Janeiro State, Brazil...
February 3, 2018: Letters in Applied Microbiology
Larry K Kociolek, Dale N Gerding, David W Hecht, Egon A Ozer
Clostridium difficile PCR ribotype 106 (also identified as restriction endonuclease analysis [REA] group DH) recently emerged as the most common strain causing C. difficile infection (CDI) among US adults. We previously identified this strain predominating our pediatric cohort. Pediatric clinical CDI isolates previously characterized by REA underwent antibiotic resistance testing and whole genome sequencing. Of 134 isolates collected from children, 31 (23%) were REA group DH. We performed a comparative genomics analysis to identify DH-associated accessory genes...
January 29, 2018: Microbes and Infection
Rohan Maddamsetti, Richard E Lenski
Few experimental studies have examined the role that sexual recombination plays in bacterial evolution, including the effects of horizontal gene transfer on genome structure. To address this limitation, we analyzed genomes from an experiment in which Escherichia coli K-12 Hfr (high frequency recombination) donors were periodically introduced into 12 evolving populations of E. coli B and allowed to conjugate repeatedly over the course of 1000 generations. Previous analyses of the evolved strains from this experiment showed that recombination did not accelerate adaptation, despite increasing genetic variation relative to asexual controls...
January 31, 2018: PLoS Genetics
Adam Peritz, George C Paoli, Chin-Yi Chen, Andrew G Gehring
DNA sequencing and other DNA-based methods are now broadly used for detection and identification of bacterial foodborne pathogens. For the identification of foodborne bacterial pathogens, taxonomic assignments must be made to the species or even subspecies level. Long-read DNA sequencing provides finer taxonomic resolution than short-read sequencing. Here, we demonstrate the potential of long-read shotgun sequencing obtained from the Oxford Nanopore Technologies (ONT) MinION single-molecule sequencer, in combination with the Basic Local Alignment Search Tool (BLAST) with custom sequence databases, for foodborne pathogen identification...
January 27, 2018: Analytical and Bioanalytical Chemistry
Beatriz Chueca, Adriana Renzoni, Daniel Berdejo, Rafael Pagán, William L Kelley, Diego García-Gonzalo
Food preservation by the use of essential oils (EOs) is being extensively studied, because of the antimicrobial properties of their individual constituents (ICs). Three resistant mutants (termed CAR, CIT and LIM) of Escherichia coli MG1655 were selected by subculturing with the ICs carvacrol, citral and (+)-limonene oxide, respectively. These derivative strains showed increased MIC values to ICs and concomitant enhanced resistance to various antibiotics (ampicillin, trimethoprim, chloramphenicol, tetracycline, kanamycin, novobiocin, norfloxacin, cephalexin and nalidixic acid) compared with the parental strain (WT)...
January 26, 2018: Applied and Environmental Microbiology
Garold Fuks, Michael Elgart, Amnon Amir, Amit Zeisel, Peter J Turnbaugh, Yoav Soen, Noam Shental
BACKGROUND: Most of our knowledge about the remarkable microbial diversity on Earth comes from sequencing the 16S rRNA gene. The use of next-generation sequencing methods has increased sample number and sequencing depth, but the read length of the most widely used sequencing platforms today is quite short, requiring the researcher to choose a subset of the gene to sequence (typically 16-33% of the total length). Thus, many bacteria may share the same amplified region, and the resolution of profiling is inherently limited...
January 26, 2018: Microbiome
Nguyen Duc Toan, Thomas C Darton, Christine J Boinett, James I Campbell, Abhilasha Karkey, Evelyne Kestelyn, Le Quoc Thinh, Nguyen Kien Mau, Pham Thi Thanh Tam, Le Nguyen Thanh Nhan, Ngo Ngoc Quang Minh, Cam Ngoc Phuong, Nguyen Thanh Hung, Ngo Minh Xuan, Tang Chi Thuong, Stephen Baker
INTRODUCTION: The clinical syndrome of neonatal sepsis, comprising signs of infection, septic shock and organ dysfunction in infants ≤4 weeks of age, is a frequent sequel to bloodstream infection and mandates urgent antimicrobial therapy. Bacterial characterisation and antimicrobial susceptibility testing is vital for ensuring appropriate therapy, as high rates of antimicrobial resistance (AMR), especially in low-income and middle-income countries, may adversely affect outcome. Ho Chi Minh City (HCMC) in Vietnam is a rapidly expanding city in Southeast Asia with a current population of almost 8 million...
January 24, 2018: BMJ Open
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